Download Students know DNA molecules provide instructions for assembling

Performance Benchmark L.12.A.2
Students know DNA molecules provide instructions for assembling protein molecules. E/S
In summarizing the findings of their 1938 experiment Beadle and Tatum made the
statement “one gene, one enzyme”. In this experiment Beadle and Tatum concluded that
the genes in the DNA molecule were responsible for the coding of enzymes, a type of
protein. Today we also know that the genes in DNA also code other proteins such as
melanin, (a pigment found in our skin, hair and eyes) and insulin (a hormone involved in
the regulation of blood sugar).
Each cell contains just one copy of the genetic information which codes for the hundreds
of proteins needed by the cell at any given moment. Thus the process of coding for
proteins needs many messengers to be delivered to the hundreds of ribosomes that are
actively making these proteins. This process is a part of what Watson and Crick first
proposed as the “Central Dogma.” In this process DNA makes a molecule called
messenger RNA (mRNA) which delivers the genetic code to the ribosomes, which
translates the code into proteins.
Figure 1: The Central Dogma of Molecular Genetics
http://www.emc.maricopa.edu/faculty/farabee/biobk/BioBookPROTSYn.html
To learn more about the Central Dogma of biology go to
http://web.mit.edu/esgbio/www/dogma/dogma.html
or http://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology
During the process of transcription one strand of DNA that contains the gene serves as a
template to form mRNA. But unlike replication where thymine serves as the
complementary base to adenine, uracil another pyrimidine base substitutes for thymine.
Guanine and cytosine still pair. Once this complementary strand of mRNA is produced,
the process is not finished as will be discussed later.
Figure 2. Transcription of RNA
http://library.thinkquest.org/C0123260/basic%20knowledge/images/basic%20knowledge/RNA/transcriptio
n.jpg
Biologists have learned that not all of the DNA present codes for proteins. In the case of
humans it now appears that as little as 1.5% of bases in human DNA actually code for
proteins. They have discovered that the DNA sequences that forms our genes and code
for proteins are divided into exons (the meaningful or coded segments) and introns (the
interrupting or noncoded segments). These introns will be cut out after the initial mRNA
molecule is made. Afterwards the exons are joined forming the mRNA sequence that will
code for the protein formation. This process is illustrated in Figure 3. Special enzymes
called splicosomes help in the removal of the introns.
Figure 3. RNA splicing – removing the introns
http://www.accessexcellence.org/RC/VL/GG/images/rna_synth.gif
To learn more about transcription go to
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html
To view animations of transcription go to
http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.swf
or http://highered.mcgraw-hill.com/olc/dl/120077/bio30.swf
One of the major findings of the Human Genome Projects is that, at least in humans,
these exons can be rearranged. Therefore one gene can actually be responsible for coding
for two or three different, but related proteins. This also might explain why the number of
genes in humans (approximately 20,000-25,000) is so small as compared to other
organisms as C . elegans a “simple” roundworm that has about 19,000 genes.
Figure 4. The alternative arranging of exons.
http://www.plantgdb.org/tutorial/annotatemodule/images/alternativesplicing.jpg
In the formation of RNA the cell can actually make three types. As discussed above
mRNA will carry the genetic code for a particular protein from the nucleus to the
ribosomes where proteins are made in the cell. Two other types of RNA are also made
from genetic code in the DNA. Ribosomal RNA (rRNA) is used along with other proteins
to construct the ribosomes. A third called transfer RNA (tRNA) is formed and will carry
amino acids from sources in the cytoplasm to the ribosomes during protein synthesis.
To learn more about the three types of RNA go to
http://www.elmhurst.edu/~chm/vchembook/583rnatypes.html
In the process of translation or protein synthesis, ribosomes read the coded message in
mRNA. As the message is read another form of RNA called transfer RNA (tRNA)
delivers amino acids to the ribosomes. The ribosome themselves are formed from
proteins and a third type of RNA called ribosomal RNA (rRNA). Note the illustration
below.
The process can be divided into 4 stages:
1. Initiation – binding of mRNA, ribosomal subunit, and tRNA carrying methionine
2. Elongation/Translocation – the ribosome moves along the mRNA reading the
codons. The tRNAs with the appropriate complementary anticodon and amino
acids joins the ribosome. For example if the mRNA codon is AUG, the tRNA
anticodon would be UAC. As the ribosome moves along the mRNA, new tRNA
molecule with complementary anticodons enter the ribosome. Amino acids are
joined and the new protein continues to grow.
Figure 5: http://library.thinkquest.org/18617/media/anticodon.gif
3. Termination – a stop codon enters the ribosome. There is no appropriate tRNA
with an anticodon for stop codons. A releasing protein now enters the ribosome
rather a tRNA. Translation stops.
4. Disassembly – the ribosome subunits break apart and “falls” from the mRNA. The
new protein is released.
Figure 6: Translation or protein synthesis
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Translation.html
To view animations of translation go to
http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/translation.swf
or http://highered.mcgraw-hill.com/olc/dl/120077/micro06.swf
The mRNA may continue to be read by other ribosomes. Biologists have discovered that
often multiple ribosomes are “reading” the mRNA at any one time. These are sometimes
termed polyribosomes. This will increase the rate of protein production as the cell can
make multiple copies of the same protein at the same time.
Figure 7. Electron microgram of a polyribosome.
http://bass.bio.uci.edu/~hudel/bs99a/lecture23/polysome_only.gif
In the early 1960s the genetic code was worked out by a number of biologists. Using
mRNA these biologists were able to determine that groups of 3-bases called a codon,
code for one amino acid. The result of the work is illustrated in the table below. The first
letter of the codon identifies the row; the second letter identifies the column; while the
third letter identifies the amino acid at the intersection of the selected row and column.
For example AUG codes for methionine. AUG is most often the codon used in coding for
proteins. Notice that three codons do not code for any amino acids, but serve as stop
signals.
Figure 8. The Genetic Code – table version
http://www.emc.maricopa.edu/faculty/farabee/biobk/code.gif
The genetic code shows redundancy, that is, there are multiple codons for many of the
amino acids. One effect of this is to reduce the potential for harmful mutations.
Students might ask why the table starts with “U” rather than “A”. The answer is that the
researcher started with mRNA consisting of uracil. The codon UUU was the first to be
linked with an amino acid. The above table is the more tradition view of the genetic code,
below is a more recent view. In this table the code reads from the inside out. Therefore
the mRNA codon GAA codes for glutamic acid.
Figure 9. The Genetic Code – circle version
http://www.biology.lsu.edu/heydrjay/1201/Chapter17/SCI_Amino
_Acid_CIRCLE.jpg
To learn more about the genetic code go to
http://users.rcn.com/jkimball.ma.ultranet/BiologyPage
s/C/Codons.html
The redundancy of the genetic code as state earlier may help to reduce the effect of DNA
base mutations. Single base errors in DNA copying are called point mutations, but are
rare. During DNA replication the error rate is 1 in 10,000 bases being copied. Most of
these errors are corrected by DNA proof readers. Secondly if an error is not corrected, the
redundancy of the genetic code may end up coding for the same amino acid. (See the
table below.) This is called a silent mutation. Or an amino acid with similar properties
can be coded for by the “mutant” codon which is sometimes called a neutral mutation.
(See the table below.)
At the same time some point mutations can be harmful. In the table below the DNA
triplet and mRNA codon are shown for the 6th amino acid for normal hemoglobin. In
sickle-cell anemia a mutation from T to A leads to the replacing of glutamic acid with
valine. This is called a missence mutation as the new protein does not function normally.
This can be seen in sickle cell anemia. The effect of this mutation occurs when the
oxygen levels in the blood drop, as during heavy exercise. When these low oxygen levels
occur, the hemoglobin will become abnormally shaped, which in turn “stretches” the red
blood cell. These abnormal red blood cells may cause blockage of blood vessels which
can be fatal. Additionally if the first C is replaced by A, the result is the termination of
protein synthesis and no hemoglobin molecule is produced. This is called a nonsense
mutation.
DNA
Triplet
CTC
CTT
CTA
CAC
ATC
mRNA
codon
GAG
GAA
GAU
GUG
UAG
Amino Acid
Properties
Mutation Type
Glutamic acid
Glutamic acid
Aspartic acid
Valine
Stop
Hydrophobic
Hydrophobic
Hydrophobic
Hydrophilic
Termination
Normal codon
Neutral
Silent
Missense
Nonsense
To learn more about DNA mutations go to
http://www.genetichealth.com/G101_Changes_in_DNA.shtml#Anchor2
http://evolution.berkeley.edu/evolibrary/article/0_0_0/mutations_01
Performance Benchmark L.12.A.2
Students know DNA molecules provide instructions for assembling protein molecules. E/S
Common misconceptions associate with this benchmark:
1. Students incorrectly believe that DNA is the same in all organisms.
Scientists have discovered that the four bases (adenine, guanine, thymine and cytosine) of
DNA are common to living organisms on our planet, whether they are a bacterium
causing a sore throat, to the rose we give on Valentine’s Day to the DNA found in our
bodies. And while in most organisms the DNA triplet of TAC codes for methionine, not
all the triplets code for the same amino acids in all organisms. Among the first
differences discovered were in the DNA found in the mitochondria and certain microbes.
In vertebrate mitochondria DNA the triplet ATA codes for methionine but in some other
organisms they do not. As such teachers should avoid calling the genetic code
“universal”.
Variations to the genetic code can be found at:
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2
2. Students incorrectly assume that gene pairing in DNA and RNA are the same.
While true in the case of the paring of guanine and cytosine, this is not case for adenine
and thymine. The A-T pairing occurs in DNA, but the base uracil replaces thymine in
RNA. In RNA the pairing is A-U. Thus if the DNA triplet is ATC the complementary
RNA codon will be UAG.
A base pairing activity can be found at
http://learn.genetics.utah.edu/units/basics/transcribe/
3. Students incorrectly think all the bases in DNA code for proteins.
Scientists have learned that approximately 1.5% of our DNA actually codes for proteins.
The other 98.5% is sometimes referred as “DNA junk” or “DNA gibberish”. Over 50% of
this non-coding DNA consists of repeating sequences sometimes 100s or 1000s of
nucleotides long. Other sequences act as promoters (DNA sequences that attract the
molecules that are necessary for replication and transcription) and genes for ribosomal
RNA and transfer RNA.
To learn more about findings of the Human Genome Project go to
http://biology.about.com/library/bldnamodels.htm
4. Students incorrectly think that one gene codes for only one protein.
This idea was believed to be true up until recently, but with discovers in the Humane
Genome Project scientists have found otherwise. In humans it is now know that one gene
may be responsible for the production of two or three different proteins. This occurs
when the introns (non-coding regions of DNA) are removed from mRNA after
transcription. The remaining exons (coding regions of DNA) can be rearranged to
produce different codon sequences and therefore different proteins.
To learn more about RNA processing go to
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html
5. Students incorrectly believe DNA is the genetic code for all organisms.
While true for all eukaryotes and prokaryotes, the exception includes viruses. While one
can debate the status of viruses as an organism, but with retroviruses such as HIV (human
immunodeficiency virus) use RNA rather than DNA. Once the virus invades a host
enzymes called reverse transcriptase converts the viral RNA to host DNA. Later this
DNA can be “switched on” and will produce new viruses.
To learn more about HIV and view an animation of the HIV life cycle go to
http://www.hopkins-aids.edu/hiv_lifecycle/hivcycle_txt.html
6. Students incorrectly think mutations in DNA are always harmful.
All humans with blood type O are carrying a mutation. The genes for blood type code for
proteins found on the red blood cell. Many inherit the genes for the A and B proteins.
However due to a point mutation in our ancestral past the coding for these proteins was
lost, thus those who inherit the alleles for O lack coding for either protein.
At the same time mutations might be harmful to some, but prove a benefit to the majority
of a population. As discussed above sickle cell anemia can prove to be fatal for those who
have this disease. Yet, carriers of this disease (you only have 1 defective gene and not
two) do not contract malaria which is the leading cause of death in the tropics.
While many DNA mutations may prove lethal, genetics mutations are also the ultimate
source of news genes that might occur in species. These new gene can prove beneficial if
the help a species to better adapt to its environment.
To learn more about the effects of mutations go to:
http://www.talkorigins.org/faqs/mutations.html
Performance Benchmark L.12.A.2
Students know DNA molecules provide instructions for assembling protein molecules. E/S
Sample Test Questions
Genetic Code: mRNA Codons
1. Using the Genetic Code table determine the amino acids that would be coded for by
the following mRNA sequence: CUCAAGUGCUUC?
a. Val—Tyr—Arg—Gly
b. Val—Asp—Pro—His
c. Leu—Leu—Gly—Asp
d. Leu—Lys—Cys—Phe
2. What is the DNA sequence for the following mRNA sequence: CUCAAGUGCUUC?
a. CUCAAGUGCUUC
b. GAGUUCACGAAG
c. GAGTTCACGAAG
d. AGACCTGTAGGA
3. What type of mutation occurs when the new amino acid in the sequence is different,
but has the same chemical properties?
a. Silent
b. Neutral
c. Missense
d. Nonsense
4. If the base sequence in mRNA is AUC, the tRNA sequence is
a. AUC
b. ATC
c. UAG
d. TAG
5. The sequence of nitrogenous bases in mRNA is
a. identical to the template strand of DNA on which it forms.
b. complementary to the template strand of DNA on which it forms.
c. determined by the sequence of bases in tRNA
d. complementary to the sequence of bases found in the ribosome.
6. Which of the following is NOT a structural difference between RNA and DNA?
a. A DNA molecule has two strands, while RNA has one strand.
b. DNA contains the base thymine, while RNA contains the base uracil.
c.The sugar in DNA is deoxyribose, while in RNA it is ribose.
d. Because of their sizes DNA can the leave the nucleus and RNA cannot.
7. Amino acid is carried to the ribosomes by the
a. messenger RNA.
b. ribosomal RNA.
c. transfer RNA.
d. coded RNA.
Performance Benchmark L.12.A.2
Students know DNA molecules provide instructions for assembling protein molecules. E/S
Answers to Sample Test Questions
1.
2.
3.
4.
5.
6.
7.
(d)
(c)
(b)
(c)
(b)
(d)
(c)
Performance Benchmark L.12.A.2
Students know DNA molecules provide instructions for assembling protein molecules. E/S
Intervention Strategies and Resources
The following list of intervention strategies and resources will facilitate student
understanding of this benchmark.
1. The Dolan DNA Learning Center provides a number of activities, animations and
other resources for the teacher. The DNA Teacher Guide is of particular interest to
teachers. At this site “The chromosome 11 Flyover” gives students a “tour” of the tip
of chromosome 11 and 28 genes found in this region along with other types of DNA
such as repeats and introns.
To review what is available at The Dolan DNA Learning Center go to
http://www.dnalc.org/home.html
2. DNA and RNA pairing excercise
To reinforce the pairing of bases in DNA and RNA the teacher can provide this paper
and pencil exercises. Give students a “sample” DNA sequence such as
TACCAGCTTCAA and have the student determine the complementary DNA strand.
Next have them produce the mRNA code and use the Genetic Code table to determine
the amino acid that this mRNA would produce. A coloring exercise similar to this can
be found the website below.
To utilize a paper and pencil coding exercise go to
http://www.biologycorner.com/worksheets/DNAcoloring.html
3. The PBS series DNA can be used by teacher looking for audio visual aids. At their
DNA series webpage are lesson plans for using this series in the classroom. Teacher
will need a copy of this series, but if not available there are interactive audio visual
activities that at its homepage.
To utilize an interactive base pairing exercise at the DNA Workshop found at PBS go
to http://www.pbs.org/wgbh/aso/tryit/dna/index.html
To learn more about this series go to
http://www.pbs.org/wnet/dna/
4. Photo 51 Activity - Another PBS show that can be used by teachers is the Nova
program Secret of Photo 51. This show traces the efforts by Rosalind Franklin to
unlock the secrets of DNA’s structure. In particular an interactive activity explains
the use of X-ray diffraction and how this famous photo 51 was used to determine the
shape and dimensions of DNA
To use this activity at the Photo 51 site go to
http://www.pbs.org/wgbh/nova/photo51/
5. The Genetics Learning Center also has an interactive computer activity that allows
student to transcribe and translate a gene.
To use this activity go to
http://learn.genetics.utah.edu/
6. Role playing activity on transcription - For teachers who like to do role playing the
site below contains a role playing activity that involves the process of translation. In
this activity produce a section of the hemoglobin protein. The first site contains the
directions and second additional information for this activity.
To use this activity go to
http://sciencespot.net/Media/protsynoutline.pdf and
http://sciencespot.net/Media/protsyncodes.pdf